bioguider 0.2.27__py3-none-any.whl → 0.2.29__py3-none-any.whl

bioguider/generation/output_manager.py

@@ -3,14 +3,14 @@ from __future__ import annotations
 import os
 import json
 from datetime import datetime
-from typing import Dict, List, Tuple
+from typing import Dict, List, Optional, Tuple
 
 from .models import OutputArtifact, GenerationManifest, PlannedEdit
 
 
 class OutputManager:
-    def __init__(self, base_outputs_dir: str = "outputs"):
-        self.base_outputs_dir = base_outputs_dir
+    def __init__(self, base_outputs_dir: Optional[str] = None):
+        self.base_outputs_dir = base_outputs_dir or "outputs"
 
     def prepare_output_dir(self, repo_url_or_name: str) -> str:
         repo_name = self._extract_repo_name(repo_url_or_name)

bioguider/generation/report_loader.py

@@ -123,14 +123,17 @@ class EvaluationReportLoader:
         normalized = normalize(raw)
 
         # Special handling for stringified evaluation fields
-        inst_eval = normalized.get("installation_evaluation")
+        inst_eval = normalized.get("installation")
         if isinstance(inst_eval, str):
             normalized["installation_evaluation"] = {
-                "structured_evaluation": self._parse_structured_block(inst_eval, "structured_evaluation"),
+                "structured_evaluation": self._parse_structured_block(inst_eval["evaluation"], "structured_evaluation"),
             }
+        else:
+            normalized["installation_evaluation"] = inst_eval["evaluation"]
+            normalized["installation_files"] = inst_eval["files"]
 
-        readme_eval = normalized.get("readme_evaluation")
-        if isinstance(readme_eval, dict):
+        readme_eval = normalized.get("readme")
+        if isinstance(readme_eval["evaluations"], dict):
             fixed: Dict[str, Any] = {}
             for fname, val in readme_eval.items():
                 if isinstance(val, str):
@@ -140,10 +143,16 @@ class EvaluationReportLoader:
                 else:
                     fixed[fname] = val
             normalized["readme_evaluation"] = fixed
+            normalized["readme_files"] = readme_eval["files"]
 
-        submit_eval = normalized.get("submission_requirements_evaluation")
-        if isinstance(submit_eval, str):
-            normalized["submission_requirements_evaluation"] = self._parse_submission_eval_str(submit_eval)
+        userguide_eval = normalized.get("userguide")
+        if isinstance(userguide_eval["evaluation"], dict):
+            normalized["userguide_evaluation"] = userguide_eval["evaluation"]
+            normalized["userguide_files"] = userguide_eval["files"]
+
+        # userguide_eval = normalized.get("userguide")
+        # if isinstance(userguide_eval, str):
+        #     normalized["userguide_evaluation"] = self._parse_structured_block(userguide_eval["evaluation"], "structured_evaluation")
 
         report = EvaluationReport(**normalized)
         return report, report_path

bioguider/managers/generation_manager.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 import os
 from pathlib import Path
-from typing import Tuple, Dict, List
+from typing import Optional, Tuple, Dict, List
 
 from bioguider.generation import (
     EvaluationReportLoader,
@@ -20,7 +20,7 @@ from bioguider.utils.file_utils import parse_repo_url
 
 
 class DocumentationGenerationManager:
-    def __init__(self, llm, step_callback):
+    def __init__(self, llm, step_callback, output_dir: Optional[str] = None):
         self.llm = llm
         self.step_callback = step_callback
         self.repo_url_or_path: str | None = None
@@ -30,7 +30,7 @@ class DocumentationGenerationManager:
         self.style_analyzer = StyleAnalyzer()
         self.planner = ChangePlanner()
         self.renderer = DocumentRenderer()
-        self.output = OutputManager()
+        self.output = OutputManager(base_outputs_dir=output_dir)
         self.llm_gen = LLMContentGenerator(llm)
         self.llm_cleaner = LLMCleaner(llm)
 

{bioguider-0.2.27.dist-info → bioguider-0.2.29.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioguider
-Version: 0.2.27
+Version: 0.2.29
 Summary: An AI-Powered package to help biomedical developers to generate clear documentation
 License: MIT
 Author: Cankun Wang

{bioguider-0.2.27.dist-info → bioguider-0.2.29.dist-info}/RECORD

@@ -49,14 +49,14 @@ bioguider/generation/llm_cleaner.py,sha256=aMxc3j6IH_9mCfBjxY1bn0bAUtUkUoHjumobz
 bioguider/generation/llm_content_generator.py,sha256=1pfXYRykvGgLGu9YJH-DhvaMzb7hy_EyvHQ8XojUBQ8,3684
 bioguider/generation/llm_injector.py,sha256=bVxP6Asv2em4MBOB5yFsS14AuaeT7NLKQQMcsEqXjPY,17352
 bioguider/generation/models.py,sha256=q9sF32Iu5VAa59UbheqPWEZn4bYeGGUVzpW24NJR_SM,2518
-bioguider/generation/output_manager.py,sha256=V0eXYG9iaWxUjU44eLLX5mQcfjOz5tAKa_X0rkTc5Aw,1935
+bioguider/generation/output_manager.py,sha256=uwLyavND4kXOHlsXB0Berab3y8u6bhaEmQOQLl7wDAM,1963
 bioguider/generation/repo_reader.py,sha256=ivTURU61fR8er4ev7gSpOxER3FJv2d9GAx_X5JoVTvQ,1177
-bioguider/generation/report_loader.py,sha256=KtJ6JHGPDL-PQoucU8hkVzMSz-B0bHbF2WShjuz2fY8,5102
+bioguider/generation/report_loader.py,sha256=m6_zcXsm5X6cFUB0ypVo1rjwjQzPAwwg83tc4H0X_eA,5598
 bioguider/generation/style_analyzer.py,sha256=Vn9FAK1qJBNLolLC1tz362k4UBaPl107BlvkQc8pV2I,983
 bioguider/generation/suggestion_extractor.py,sha256=tfkyWtdbAo-maLCF_wqwBXyh93yjulvDY17FuvTnTjk,7611
 bioguider/generation/test_metrics.py,sha256=ACXmSZc2L_UkkmC5h2s4tG44MXW1d-hClFwPCD5_BFI,7505
 bioguider/managers/evaluation_manager.py,sha256=EoZ8V4rmx16zk1J3N9cNjeo0aCa7i32fLEQ3b2UolEQ,5917
-bioguider/managers/generation_manager.py,sha256=p2c569lams5-_WYHdynBpVap8gKtQPxQEcZOrPllNuY,9523
+bioguider/managers/generation_manager.py,sha256=94Fe-0q37t7QIP2lkdmEiTjb8-hbiz9XX9h8Gi6BkSU,9594
 bioguider/managers/generation_test_manager.py,sha256=3mOBzQVpsLo_LpSspJcofn3CNtvgagS1DMr9Zuwkzq4,5307
 bioguider/rag/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioguider/rag/config.py,sha256=5g4IqTzgyfZfax9Af9CTkXShgItPOt4_9TEMSekCPik,4602
@@ -74,7 +74,7 @@ bioguider/utils/pyphen_utils.py,sha256=cdZc3qphkvMDeL5NiZ8Xou13M_uVNP7ifJ-FwxO-0
 bioguider/utils/python_file_handler.py,sha256=BERiE2RHxpu3gAzv26jr8ZQetkrtnMZOv9SjpQ7WIdg,2650
 bioguider/utils/r_file_handler.py,sha256=8HpFaYKP8N1nItwr9tOx49m99pcLSt8EUtTNTJ7xNoE,19564
 bioguider/utils/utils.py,sha256=h8OhCjzLpHkb3ndnjRBUOBHD7csbHdEVNXf75SRN8Zc,4413
-bioguider-0.2.27.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
-bioguider-0.2.27.dist-info/METADATA,sha256=NGUDYKPULcLif4PFGOTPpgXeeIILDsHT6-fu4Gh204o,1962
-bioguider-0.2.27.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-bioguider-0.2.27.dist-info/RECORD,,
+bioguider-0.2.29.dist-info/LICENSE,sha256=qzkvZcKwwA5DuSuhXMOm2LcO6BdEr4V7jwFZVL2-jL4,1065
+bioguider-0.2.29.dist-info/METADATA,sha256=O4IRhR2hhEuFMeWOYCSeQvyKHZUdWdGosGssGN0gohs,1962
+bioguider-0.2.29.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+bioguider-0.2.29.dist-info/RECORD,,